Starting phenix.real_space_refine on Tue Aug 26 04:21:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yga_39240/08_2025/8yga_39240.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yga_39240/08_2025/8yga_39240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yga_39240/08_2025/8yga_39240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yga_39240/08_2025/8yga_39240.map" model { file = "/net/cci-nas-00/data/ceres_data/8yga_39240/08_2025/8yga_39240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yga_39240/08_2025/8yga_39240.cif" } resolution = 4.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 21448 2.51 5 N 5344 2.21 5 O 6220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33140 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 8285 Classifications: {'peptide': 995} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 975} Chain: "B" Number of atoms: 8285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 8285 Classifications: {'peptide': 995} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 975} Chain: "C" Number of atoms: 8285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 8285 Classifications: {'peptide': 995} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 975} Chain: "D" Number of atoms: 8285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 8285 Classifications: {'peptide': 995} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 975} Time building chain proxies: 7.43, per 1000 atoms: 0.22 Number of scatterers: 33140 At special positions: 0 Unit cell: (100.43, 128.65, 278.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 6220 8.00 N 5344 7.00 C 21448 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.03 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 1.2 microseconds 7944 Ramachandran restraints generated. 3972 Oldfield, 0 Emsley, 3972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7568 Finding SS restraints... Secondary structure from input PDB file: 251 helices and 10 sheets defined 70.4% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 Processing helix chain 'A' and resid 23 through 39 Processing helix chain 'A' and resid 47 through 54 removed outlier: 3.607A pdb=" N SER A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 70 removed outlier: 3.849A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A 70 " --> pdb=" O TYR A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 96 Proline residue: A 88 - end of helix removed outlier: 3.775A pdb=" N GLY A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 107 removed outlier: 4.080A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.837A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 removed outlier: 3.897A pdb=" N THR A 140 " --> pdb=" O ASN A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.779A pdb=" N ASP A 157 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL A 158 " --> pdb=" O GLU A 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 158' Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 197 through 210 Processing helix chain 'A' and resid 222 through 236 Processing helix chain 'A' and resid 254 through 264 removed outlier: 3.654A pdb=" N LEU A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.786A pdb=" N LEU A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 317 removed outlier: 3.792A pdb=" N VAL A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE A 309 " --> pdb=" O ASP A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 321 removed outlier: 4.119A pdb=" N ALA A 321 " --> pdb=" O PRO A 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 318 through 321' Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.608A pdb=" N LYS A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 335 removed outlier: 3.936A pdb=" N GLU A 335 " --> pdb=" O HIS A 332 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 332 through 335' Processing helix chain 'A' and resid 355 through 366 removed outlier: 3.618A pdb=" N PHE A 361 " --> pdb=" O MET A 357 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 375 through 392 removed outlier: 4.225A pdb=" N GLU A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE A 381 " --> pdb=" O GLN A 377 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 417 through 426 removed outlier: 3.546A pdb=" N MET A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A 423 " --> pdb=" O ASP A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 446 Processing helix chain 'A' and resid 447 through 463 removed outlier: 3.766A pdb=" N LEU A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE A 463 " --> pdb=" O ILE A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 496 removed outlier: 3.601A pdb=" N TYR A 472 " --> pdb=" O GLY A 468 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 509 through 522 removed outlier: 3.581A pdb=" N ALA A 513 " --> pdb=" O ASP A 509 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ARG A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 525 No H-bonds generated for 'chain 'A' and resid 523 through 525' Processing helix chain 'A' and resid 526 through 531 Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 540 through 544 removed outlier: 3.594A pdb=" N GLU A 543 " --> pdb=" O LYS A 540 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 540 through 544' Processing helix chain 'A' and resid 548 through 552 Processing helix chain 'A' and resid 554 through 572 removed outlier: 3.792A pdb=" N LYS A 564 " --> pdb=" O GLU A 560 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER A 570 " --> pdb=" O ARG A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 599 Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.806A pdb=" N VAL A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 629 removed outlier: 3.719A pdb=" N HIS A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR A 628 " --> pdb=" O GLU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 640 removed outlier: 3.572A pdb=" N GLY A 640 " --> pdb=" O PHE A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 659 removed outlier: 3.781A pdb=" N HIS A 658 " --> pdb=" O ASN A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 671 removed outlier: 3.702A pdb=" N LEU A 667 " --> pdb=" O ASP A 663 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 668 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG A 669 " --> pdb=" O LYS A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 676 removed outlier: 3.807A pdb=" N ILE A 676 " --> pdb=" O ILE A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 699 Processing helix chain 'A' and resid 705 through 723 removed outlier: 3.934A pdb=" N THR A 710 " --> pdb=" O VAL A 706 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 718 " --> pdb=" O SER A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'A' and resid 729 through 743 removed outlier: 3.579A pdb=" N LEU A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 763 removed outlier: 3.651A pdb=" N LYS A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 786 removed outlier: 3.827A pdb=" N ILE A 774 " --> pdb=" O SER A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 812 removed outlier: 3.971A pdb=" N TYR A 804 " --> pdb=" O TYR A 800 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 825 removed outlier: 3.687A pdb=" N LEU A 825 " --> pdb=" O SER A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 840 Processing helix chain 'A' and resid 846 through 856 Processing helix chain 'A' and resid 861 through 863 No H-bonds generated for 'chain 'A' and resid 861 through 863' Processing helix chain 'A' and resid 864 through 871 removed outlier: 3.585A pdb=" N ILE A 869 " --> pdb=" O LEU A 865 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 870 " --> pdb=" O MET A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 903 removed outlier: 3.519A pdb=" N GLU A 901 " --> pdb=" O ILE A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 922 Processing helix chain 'A' and resid 928 through 933 removed outlier: 3.929A pdb=" N GLU A 932 " --> pdb=" O SER A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 950 through 954 removed outlier: 3.600A pdb=" N LYS A 953 " --> pdb=" O ASP A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 961 removed outlier: 3.631A pdb=" N LYS A 960 " --> pdb=" O SER A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 972 Processing helix chain 'A' and resid 976 through 991 Processing helix chain 'A' and resid 993 through 1003 removed outlier: 4.523A pdb=" N LEU A 997 " --> pdb=" O ASP A 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 20 Processing helix chain 'B' and resid 23 through 39 removed outlier: 3.507A pdb=" N VAL B 27 " --> pdb=" O ASP B 23 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU B 28 " --> pdb=" O ASN B 24 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N CYS B 29 " --> pdb=" O ASN B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 54 removed outlier: 3.711A pdb=" N SER B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU B 53 " --> pdb=" O GLY B 49 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 71 Processing helix chain 'B' and resid 85 through 96 removed outlier: 4.224A pdb=" N GLN B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 109 removed outlier: 3.778A pdb=" N PHE B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.999A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 145 removed outlier: 3.513A pdb=" N ARG B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 removed outlier: 4.363A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 155 through 160' Processing helix chain 'B' and resid 179 through 183 Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 197 through 211 removed outlier: 3.563A pdb=" N SER B 201 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 236 removed outlier: 3.597A pdb=" N MET B 227 " --> pdb=" O TYR B 223 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS B 234 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 235 " --> pdb=" O TRP B 231 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN B 236 " --> pdb=" O VAL B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 Processing helix chain 'B' and resid 281 through 295 removed outlier: 3.643A pdb=" N LEU B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 317 removed outlier: 3.701A pdb=" N VAL B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B 309 " --> pdb=" O ASP B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 322 removed outlier: 3.612A pdb=" N ALA B 321 " --> pdb=" O PRO B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 334 removed outlier: 3.884A pdb=" N VAL B 333 " --> pdb=" O ASP B 329 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 329 through 334' Processing helix chain 'B' and resid 355 through 366 removed outlier: 3.730A pdb=" N PHE B 361 " --> pdb=" O MET B 357 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 372 Processing helix chain 'B' and resid 376 through 392 removed outlier: 4.208A pdb=" N ARG B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 400 Processing helix chain 'B' and resid 411 through 416 removed outlier: 3.649A pdb=" N HIS B 415 " --> pdb=" O SER B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 426 removed outlier: 3.983A pdb=" N MET B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 462 removed outlier: 3.628A pdb=" N SER B 451 " --> pdb=" O ARG B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 496 Processing helix chain 'B' and resid 497 through 499 No H-bonds generated for 'chain 'B' and resid 497 through 499' Processing helix chain 'B' and resid 508 through 520 Processing helix chain 'B' and resid 523 through 525 No H-bonds generated for 'chain 'B' and resid 523 through 525' Processing helix chain 'B' and resid 526 through 531 Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 540 through 546 removed outlier: 4.172A pdb=" N PHE B 544 " --> pdb=" O ILE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 559 removed outlier: 3.764A pdb=" N PHE B 559 " --> pdb=" O THR B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 562 No H-bonds generated for 'chain 'B' and resid 560 through 562' Processing helix chain 'B' and resid 566 through 572 Processing helix chain 'B' and resid 579 through 598 Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.772A pdb=" N VAL B 603 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 621 Processing helix chain 'B' and resid 633 through 639 removed outlier: 3.907A pdb=" N SER B 637 " --> pdb=" O GLU B 633 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE B 638 " --> pdb=" O LEU B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 658 Processing helix chain 'B' and resid 660 through 671 removed outlier: 3.731A pdb=" N CYS B 671 " --> pdb=" O LEU B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 680 through 700 removed outlier: 3.584A pdb=" N ILE B 684 " --> pdb=" O GLU B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 723 removed outlier: 3.599A pdb=" N GLN B 711 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 729 through 744 removed outlier: 3.919A pdb=" N LYS B 735 " --> pdb=" O GLU B 731 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE B 736 " --> pdb=" O GLY B 732 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE B 744 " --> pdb=" O LEU B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 765 removed outlier: 4.672A pdb=" N CYS B 764 " --> pdb=" O ARG B 760 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN B 765 " --> pdb=" O LEU B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 785 removed outlier: 3.540A pdb=" N ILE B 774 " --> pdb=" O SER B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 812 removed outlier: 4.090A pdb=" N TYR B 804 " --> pdb=" O TYR B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 826 removed outlier: 3.926A pdb=" N CYS B 826 " --> pdb=" O GLU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 841 removed outlier: 3.547A pdb=" N PHE B 837 " --> pdb=" O LYS B 833 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU B 841 " --> pdb=" O PHE B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 855 removed outlier: 3.585A pdb=" N SER B 855 " --> pdb=" O SER B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 871 removed outlier: 4.186A pdb=" N ASN B 867 " --> pdb=" O ASN B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 903 Processing helix chain 'B' and resid 911 through 922 Processing helix chain 'B' and resid 928 through 933 Processing helix chain 'B' and resid 937 through 945 Processing helix chain 'B' and resid 950 through 954 Processing helix chain 'B' and resid 955 through 962 Processing helix chain 'B' and resid 963 through 973 Processing helix chain 'B' and resid 975 through 991 removed outlier: 4.750A pdb=" N HIS B 979 " --> pdb=" O HIS B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1003 removed outlier: 3.534A pdb=" N LEU B 997 " --> pdb=" O ASP B 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 22 Processing helix chain 'C' and resid 23 through 39 removed outlier: 3.514A pdb=" N VAL C 27 " --> pdb=" O ASP C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 54 removed outlier: 3.777A pdb=" N SER C 51 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 82 through 96 Proline residue: C 88 - end of helix removed outlier: 3.847A pdb=" N GLY C 96 " --> pdb=" O TYR C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 108 removed outlier: 3.869A pdb=" N PHE C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 124 removed outlier: 3.849A pdb=" N ASP C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 146 Processing helix chain 'C' and resid 154 through 161 removed outlier: 4.793A pdb=" N ALA C 159 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA C 161 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 183 removed outlier: 3.580A pdb=" N ASN C 182 " --> pdb=" O LYS C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 192 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 197 through 210 Processing helix chain 'C' and resid 222 through 236 Processing helix chain 'C' and resid 254 through 265 removed outlier: 3.553A pdb=" N LEU C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 304 through 317 removed outlier: 3.728A pdb=" N VAL C 308 " --> pdb=" O LYS C 304 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE C 309 " --> pdb=" O ASP C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 322 removed outlier: 3.923A pdb=" N ALA C 321 " --> pdb=" O PRO C 318 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 322 " --> pdb=" O LEU C 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 318 through 322' Processing helix chain 'C' and resid 326 through 334 removed outlier: 3.626A pdb=" N LEU C 330 " --> pdb=" O ARG C 326 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYS C 331 " --> pdb=" O LYS C 327 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N HIS C 332 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL C 333 " --> pdb=" O ASP C 329 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE C 334 " --> pdb=" O LEU C 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 326 through 334' Processing helix chain 'C' and resid 355 through 366 Processing helix chain 'C' and resid 368 through 372 Processing helix chain 'C' and resid 375 through 392 removed outlier: 4.167A pdb=" N GLU C 379 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE C 381 " --> pdb=" O GLN C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 416 Processing helix chain 'C' and resid 417 through 426 removed outlier: 4.039A pdb=" N MET C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 446 Processing helix chain 'C' and resid 447 through 462 Processing helix chain 'C' and resid 468 through 496 removed outlier: 3.617A pdb=" N TYR C 472 " --> pdb=" O GLY C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 500 Processing helix chain 'C' and resid 508 through 520 removed outlier: 3.549A pdb=" N THR C 520 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 531 Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 549 through 554 removed outlier: 4.394A pdb=" N ASP C 554 " --> pdb=" O PHE C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 572 removed outlier: 3.990A pdb=" N LYS C 564 " --> pdb=" O GLU C 560 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER C 570 " --> pdb=" O ARG C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 598 Processing helix chain 'C' and resid 600 through 604 removed outlier: 3.860A pdb=" N VAL C 603 " --> pdb=" O LEU C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 629 removed outlier: 3.888A pdb=" N HIS C 609 " --> pdb=" O PHE C 605 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR C 628 " --> pdb=" O GLU C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 640 removed outlier: 3.522A pdb=" N GLY C 640 " --> pdb=" O PHE C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 658 Processing helix chain 'C' and resid 660 through 671 Processing helix chain 'C' and resid 672 through 676 Processing helix chain 'C' and resid 680 through 699 Processing helix chain 'C' and resid 705 through 723 removed outlier: 3.863A pdb=" N THR C 710 " --> pdb=" O VAL C 706 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLN C 711 " --> pdb=" O VAL C 707 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER C 714 " --> pdb=" O THR C 710 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU C 715 " --> pdb=" O GLN C 711 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA C 718 " --> pdb=" O SER C 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 726 No H-bonds generated for 'chain 'C' and resid 724 through 726' Processing helix chain 'C' and resid 729 through 743 removed outlier: 3.780A pdb=" N ILE C 736 " --> pdb=" O GLY C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 763 removed outlier: 3.696A pdb=" N LYS C 763 " --> pdb=" O GLU C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 786 Processing helix chain 'C' and resid 800 through 812 removed outlier: 3.845A pdb=" N TYR C 804 " --> pdb=" O TYR C 800 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 825 removed outlier: 3.666A pdb=" N LEU C 825 " --> pdb=" O SER C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 840 Processing helix chain 'C' and resid 847 through 856 Processing helix chain 'C' and resid 861 through 863 No H-bonds generated for 'chain 'C' and resid 861 through 863' Processing helix chain 'C' and resid 864 through 871 removed outlier: 3.510A pdb=" N ARG C 870 " --> pdb=" O MET C 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 903 removed outlier: 3.523A pdb=" N GLU C 901 " --> pdb=" O ILE C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 922 Processing helix chain 'C' and resid 928 through 933 removed outlier: 4.046A pdb=" N GLU C 932 " --> pdb=" O SER C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 945 Processing helix chain 'C' and resid 950 through 954 removed outlier: 3.887A pdb=" N LYS C 953 " --> pdb=" O ASP C 950 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 962 removed outlier: 3.539A pdb=" N LYS C 960 " --> pdb=" O SER C 957 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR C 962 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 973 Processing helix chain 'C' and resid 975 through 990 removed outlier: 4.676A pdb=" N HIS C 979 " --> pdb=" O HIS C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1003 removed outlier: 4.281A pdb=" N LEU C 997 " --> pdb=" O ASP C 993 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR C1003 " --> pdb=" O ILE C 999 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 22 Processing helix chain 'D' and resid 23 through 39 removed outlier: 3.518A pdb=" N CYS D 29 " --> pdb=" O ASN D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 54 removed outlier: 4.167A pdb=" N SER D 51 " --> pdb=" O GLY D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 71 removed outlier: 3.952A pdb=" N LEU D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 96 Processing helix chain 'D' and resid 96 through 109 removed outlier: 3.768A pdb=" N PHE D 100 " --> pdb=" O GLY D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 124 removed outlier: 3.946A pdb=" N ASP D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 145 removed outlier: 3.610A pdb=" N ARG D 145 " --> pdb=" O ALA D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 160 removed outlier: 3.970A pdb=" N ALA D 159 " --> pdb=" O GLU D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 177 removed outlier: 4.597A pdb=" N LYS D 176 " --> pdb=" O ASP D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 183 removed outlier: 3.775A pdb=" N ASN D 182 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 192 Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 197 through 211 removed outlier: 3.784A pdb=" N HIS D 211 " --> pdb=" O ILE D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 235 removed outlier: 3.557A pdb=" N LYS D 234 " --> pdb=" O ASN D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 264 removed outlier: 3.508A pdb=" N LEU D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 281 through 296 removed outlier: 3.768A pdb=" N SER D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 317 removed outlier: 3.703A pdb=" N VAL D 308 " --> pdb=" O LYS D 304 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS D 315 " --> pdb=" O TYR D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 322 removed outlier: 3.509A pdb=" N ALA D 321 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU D 322 " --> pdb=" O LEU D 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 318 through 322' Processing helix chain 'D' and resid 329 through 334 removed outlier: 4.186A pdb=" N VAL D 333 " --> pdb=" O ASP D 329 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 329 through 334' Processing helix chain 'D' and resid 355 through 366 removed outlier: 3.766A pdb=" N PHE D 361 " --> pdb=" O MET D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 372 removed outlier: 3.559A pdb=" N LYS D 372 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 392 Processing helix chain 'D' and resid 411 through 416 removed outlier: 4.092A pdb=" N HIS D 415 " --> pdb=" O SER D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 426 removed outlier: 3.709A pdb=" N MET D 421 " --> pdb=" O LYS D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 446 Processing helix chain 'D' and resid 447 through 463 removed outlier: 3.905A pdb=" N ILE D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 496 Processing helix chain 'D' and resid 497 through 499 No H-bonds generated for 'chain 'D' and resid 497 through 499' Processing helix chain 'D' and resid 508 through 520 removed outlier: 3.503A pdb=" N LEU D 512 " --> pdb=" O THR D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 531 Processing helix chain 'D' and resid 532 through 539 Processing helix chain 'D' and resid 540 through 547 removed outlier: 4.427A pdb=" N PHE D 544 " --> pdb=" O ILE D 541 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU D 545 " --> pdb=" O LEU D 542 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER D 546 " --> pdb=" O GLU D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 562 removed outlier: 3.707A pdb=" N PHE D 559 " --> pdb=" O VAL D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 572 Processing helix chain 'D' and resid 579 through 598 Processing helix chain 'D' and resid 600 through 604 removed outlier: 3.869A pdb=" N VAL D 603 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 621 removed outlier: 3.633A pdb=" N HIS D 609 " --> pdb=" O PHE D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 633 through 639 removed outlier: 3.878A pdb=" N SER D 637 " --> pdb=" O GLU D 633 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE D 638 " --> pdb=" O LEU D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 659 removed outlier: 3.530A pdb=" N PHE D 659 " --> pdb=" O ILE D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 660 through 671 Processing helix chain 'D' and resid 672 through 676 Processing helix chain 'D' and resid 680 through 701 removed outlier: 3.651A pdb=" N ILE D 684 " --> pdb=" O GLU D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 705 through 723 removed outlier: 3.563A pdb=" N GLN D 711 " --> pdb=" O VAL D 707 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER D 714 " --> pdb=" O THR D 710 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU D 715 " --> pdb=" O GLN D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 726 No H-bonds generated for 'chain 'D' and resid 724 through 726' Processing helix chain 'D' and resid 729 through 743 Processing helix chain 'D' and resid 750 through 763 removed outlier: 3.628A pdb=" N TYR D 755 " --> pdb=" O ILE D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 769 through 786 Processing helix chain 'D' and resid 800 through 812 removed outlier: 4.120A pdb=" N TYR D 804 " --> pdb=" O TYR D 800 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE D 811 " --> pdb=" O LEU D 807 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 826 removed outlier: 3.834A pdb=" N CYS D 826 " --> pdb=" O GLU D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 833 through 839 Processing helix chain 'D' and resid 846 through 855 Processing helix chain 'D' and resid 861 through 871 removed outlier: 3.871A pdb=" N ASN D 867 " --> pdb=" O ASN D 863 " (cutoff:3.500A) Processing helix chain 'D' and resid 878 through 903 Processing helix chain 'D' and resid 911 through 922 Processing helix chain 'D' and resid 928 through 933 Processing helix chain 'D' and resid 937 through 945 Processing helix chain 'D' and resid 950 through 954 Processing helix chain 'D' and resid 955 through 962 removed outlier: 3.599A pdb=" N TRP D 958 " --> pdb=" O ILE D 955 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR D 962 " --> pdb=" O LEU D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 963 through 973 removed outlier: 3.653A pdb=" N ASN D 973 " --> pdb=" O LYS D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 975 through 990 removed outlier: 4.466A pdb=" N HIS D 979 " --> pdb=" O HIS D 975 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN D 990 " --> pdb=" O GLU D 986 " (cutoff:3.500A) Processing helix chain 'D' and resid 993 through 1003 Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 5.975A pdb=" N SER A 150 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LYS A 169 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE A 152 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL A 129 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N LEU A 42 " --> pdb=" O HIS A 128 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ILE A 130 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N PHE A 44 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL A 43 " --> pdb=" O VAL A 214 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 244 through 246 removed outlier: 6.730A pdb=" N PHE A 245 " --> pdb=" O ILE A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 338 through 340 removed outlier: 3.527A pdb=" N VAL A 346 " --> pdb=" O CYS A 395 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 150 through 152 removed outlier: 3.614A pdb=" N LYS B 169 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL B 129 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU B 42 " --> pdb=" O HIS B 128 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N ILE B 130 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE B 44 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL B 43 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE B 216 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE B 45 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 244 through 247 Processing sheet with id=AA6, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AA7, first strand: chain 'C' and resid 150 through 152 removed outlier: 5.899A pdb=" N SER C 150 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LYS C 169 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE C 152 " --> pdb=" O LYS C 169 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU C 42 " --> pdb=" O HIS C 128 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ILE C 130 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE C 44 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 338 through 340 removed outlier: 3.740A pdb=" N VAL C 346 " --> pdb=" O CYS C 395 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 150 through 152 removed outlier: 3.737A pdb=" N VAL D 129 " --> pdb=" O TYR D 166 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N HIS D 128 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL D 214 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE D 45 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE D 213 " --> pdb=" O PHE D 244 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ILE D 246 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N PHE D 215 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE D 245 " --> pdb=" O ILE D 269 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 338 through 341 removed outlier: 3.653A pdb=" N THR D 345 " --> pdb=" O GLU D 341 " (cutoff:3.500A) 1660 hydrogen bonds defined for protein. 4773 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.27 Time building geometry restraints manager: 3.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7666 1.33 - 1.45: 7703 1.45 - 1.57: 18326 1.57 - 1.70: 1 1.70 - 1.82: 216 Bond restraints: 33912 Sorted by residual: bond pdb=" N GLU C 298 " pdb=" CA GLU C 298 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.85e+00 bond pdb=" CA ARG B 145 " pdb=" C ARG B 145 " ideal model delta sigma weight residual 1.523 1.484 0.039 1.80e-02 3.09e+03 4.79e+00 bond pdb=" CA SER C 296 " pdb=" CB SER C 296 " ideal model delta sigma weight residual 1.530 1.496 0.034 1.69e-02 3.50e+03 4.12e+00 bond pdb=" C LEU B 842 " pdb=" N PRO B 843 " ideal model delta sigma weight residual 1.334 1.350 -0.016 8.40e-03 1.42e+04 3.82e+00 bond pdb=" CB PRO C 74 " pdb=" CG PRO C 74 " ideal model delta sigma weight residual 1.492 1.584 -0.092 5.00e-02 4.00e+02 3.36e+00 ... (remaining 33907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 45140 3.23 - 6.45: 454 6.45 - 9.68: 70 9.68 - 12.91: 13 12.91 - 16.13: 3 Bond angle restraints: 45680 Sorted by residual: angle pdb=" N ASN C 299 " pdb=" CA ASN C 299 " pdb=" C ASN C 299 " ideal model delta sigma weight residual 112.34 102.91 9.43 1.30e+00 5.92e-01 5.27e+01 angle pdb=" CA PRO D 532 " pdb=" N PRO D 532 " pdb=" CD PRO D 532 " ideal model delta sigma weight residual 112.00 103.22 8.78 1.40e+00 5.10e-01 3.94e+01 angle pdb=" CB MET A 616 " pdb=" CG MET A 616 " pdb=" SD MET A 616 " ideal model delta sigma weight residual 112.70 96.57 16.13 3.00e+00 1.11e-01 2.89e+01 angle pdb=" N VAL B 565 " pdb=" CA VAL B 565 " pdb=" C VAL B 565 " ideal model delta sigma weight residual 113.20 108.06 5.14 9.60e-01 1.09e+00 2.86e+01 angle pdb=" CB MET A 976 " pdb=" CG MET A 976 " pdb=" SD MET A 976 " ideal model delta sigma weight residual 112.70 127.24 -14.54 3.00e+00 1.11e-01 2.35e+01 ... (remaining 45675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 17261 17.91 - 35.83: 2301 35.83 - 53.74: 519 53.74 - 71.65: 88 71.65 - 89.57: 39 Dihedral angle restraints: 20208 sinusoidal: 8408 harmonic: 11800 Sorted by residual: dihedral pdb=" CA GLN D 297 " pdb=" C GLN D 297 " pdb=" N GLU D 298 " pdb=" CA GLU D 298 " ideal model delta harmonic sigma weight residual 180.00 129.52 50.48 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA GLN B 297 " pdb=" C GLN B 297 " pdb=" N GLU B 298 " pdb=" CA GLU B 298 " ideal model delta harmonic sigma weight residual 180.00 135.86 44.14 0 5.00e+00 4.00e-02 7.79e+01 dihedral pdb=" CA GLN D 58 " pdb=" C GLN D 58 " pdb=" N TRP D 59 " pdb=" CA TRP D 59 " ideal model delta harmonic sigma weight residual 180.00 -149.89 -30.11 0 5.00e+00 4.00e-02 3.63e+01 ... (remaining 20205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3863 0.058 - 0.115: 859 0.115 - 0.173: 93 0.173 - 0.230: 11 0.230 - 0.288: 2 Chirality restraints: 4828 Sorted by residual: chirality pdb=" CG LEU B 228 " pdb=" CB LEU B 228 " pdb=" CD1 LEU B 228 " pdb=" CD2 LEU B 228 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CG LEU A 558 " pdb=" CB LEU A 558 " pdb=" CD1 LEU A 558 " pdb=" CD2 LEU A 558 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CB THR B 696 " pdb=" CA THR B 696 " pdb=" OG1 THR B 696 " pdb=" CG2 THR B 696 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 4825 not shown) Planarity restraints: 5840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 295 " 0.025 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C GLU C 295 " -0.089 2.00e-02 2.50e+03 pdb=" O GLU C 295 " 0.034 2.00e-02 2.50e+03 pdb=" N SER C 296 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET D 531 " -0.080 5.00e-02 4.00e+02 1.15e-01 2.13e+01 pdb=" N PRO D 532 " 0.199 5.00e-02 4.00e+02 pdb=" CA PRO D 532 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO D 532 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 197 " -0.068 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO A 198 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO A 198 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 198 " -0.055 5.00e-02 4.00e+02 ... (remaining 5837 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 513 2.63 - 3.20: 32625 3.20 - 3.76: 51881 3.76 - 4.33: 69548 4.33 - 4.90: 106336 Nonbonded interactions: 260903 Sorted by model distance: nonbonded pdb=" OH TYR C 471 " pdb=" O GLY D 146 " model vdw 2.059 3.040 nonbonded pdb=" O GLU A 516 " pdb=" OG1 THR A 520 " model vdw 2.059 3.040 nonbonded pdb=" OD2 ASP D 337 " pdb=" OH TYR D 356 " model vdw 2.069 3.040 nonbonded pdb=" OE2 GLU D 516 " pdb=" OG1 THR D 520 " model vdw 2.075 3.040 nonbonded pdb=" O LYS A 41 " pdb=" OG1 THR A 212 " model vdw 2.080 3.040 ... (remaining 260898 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 30.830 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 33912 Z= 0.191 Angle : 0.856 16.133 45680 Z= 0.465 Chirality : 0.047 0.288 4828 Planarity : 0.005 0.115 5840 Dihedral : 16.941 89.565 12640 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.92 % Favored : 92.75 % Rotamer: Outliers : 0.63 % Allowed : 21.71 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.13), residues: 3972 helix: 0.27 (0.11), residues: 2326 sheet: -1.23 (0.48), residues: 110 loop : -1.55 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 517 TYR 0.050 0.002 TYR B 455 PHE 0.045 0.002 PHE D 837 TRP 0.060 0.004 TRP D 958 HIS 0.007 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00388 (33912) covalent geometry : angle 0.85582 (45680) hydrogen bonds : bond 0.15811 ( 1660) hydrogen bonds : angle 6.56969 ( 4773) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7944 Ramachandran restraints generated. 3972 Oldfield, 0 Emsley, 3972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7944 Ramachandran restraints generated. 3972 Oldfield, 0 Emsley, 3972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 704 MET cc_start: 0.7761 (tmm) cc_final: 0.7511 (tmm) REVERT: A 744 PHE cc_start: 0.7810 (t80) cc_final: 0.7270 (t80) outliers start: 6 outliers final: 2 residues processed: 82 average time/residue: 0.0981 time to fit residues: 10.8918 Evaluate side-chains 42 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.0980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.0870 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.0770 chunk 183 optimal weight: 6.9990 overall best weight: 1.0520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN C 115 ASN C 118 HIS C 133 ASN ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 HIS C 428 GLN C 548 ASN C 939 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.038487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.028661 restraints weight = 131354.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.029333 restraints weight = 82421.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.029810 restraints weight = 58973.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.030193 restraints weight = 47107.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.030365 restraints weight = 40547.759| |-----------------------------------------------------------------------------| r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 2.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 33912 Z= 0.208 Angle : 0.872 9.947 45680 Z= 0.493 Chirality : 0.049 0.272 4828 Planarity : 0.007 0.074 5840 Dihedral : 6.431 50.466 4392 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 1.41 % Allowed : 4.73 % Favored : 93.86 % Rotamer: Outliers : 0.88 % Allowed : 3.29 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.13), residues: 3972 helix: -0.17 (0.10), residues: 2528 sheet: -0.73 (0.49), residues: 108 loop : -1.46 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 657 TYR 0.034 0.002 TYR D 260 PHE 0.032 0.002 PHE D 320 TRP 0.037 0.003 TRP D 919 HIS 0.005 0.001 HIS D 67 Details of bonding type rmsd covalent geometry : bond 0.00421 (33912) covalent geometry : angle 0.87166 (45680) hydrogen bonds : bond 0.09446 ( 1660) hydrogen bonds : angle 6.16890 ( 4773) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 396 MET cc_start: 0.7010 (mmp) cc_final: 0.6708 (tpp) REVERT: C 531 MET cc_start: 0.9059 (mmm) cc_final: 0.8243 (mtp) REVERT: C 578 MET cc_start: 0.8954 (pmm) cc_final: 0.8746 (tpt) REVERT: C 659 PHE cc_start: 0.5634 (OUTLIER) cc_final: 0.5042 (m-80) outliers start: 8 outliers final: 1 residues processed: 51 average time/residue: 0.0992 time to fit residues: 6.9644 Evaluate side-chains 30 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 127 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 308 optimal weight: 0.3980 chunk 227 optimal weight: 1.9990 chunk 196 optimal weight: 10.0000 chunk 160 optimal weight: 8.9990 chunk 231 optimal weight: 30.0000 chunk 273 optimal weight: 3.9990 chunk 377 optimal weight: 0.0370 chunk 75 optimal weight: 3.9990 chunk 291 optimal weight: 4.9990 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 654 ASN C 867 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.037101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.025538 restraints weight = 114031.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.026182 restraints weight = 82408.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.026435 restraints weight = 62226.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.026811 restraints weight = 53547.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.026962 restraints weight = 47240.250| |-----------------------------------------------------------------------------| r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 2.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 33912 Z= 0.161 Angle : 0.707 9.249 45680 Z= 0.409 Chirality : 0.044 0.339 4828 Planarity : 0.005 0.051 5840 Dihedral : 5.655 32.290 4392 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.60 % Allowed : 5.14 % Favored : 94.26 % Rotamer: Outliers : 0.77 % Allowed : 3.62 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.13), residues: 3972 helix: -0.25 (0.10), residues: 2512 sheet: -0.04 (0.51), residues: 116 loop : -1.25 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 38 TYR 0.022 0.002 TYR B 260 PHE 0.025 0.002 PHE B 320 TRP 0.028 0.002 TRP B 919 HIS 0.005 0.001 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00325 (33912) covalent geometry : angle 0.70670 (45680) hydrogen bonds : bond 0.07184 ( 1660) hydrogen bonds : angle 5.64953 ( 4773) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 MET cc_start: 0.8949 (mmp) cc_final: 0.8621 (mmm) REVERT: C 227 MET cc_start: 0.9533 (ptp) cc_final: 0.9196 (ptp) REVERT: C 290 MET cc_start: 0.9626 (tpt) cc_final: 0.9347 (tpp) REVERT: C 396 MET cc_start: 0.7012 (mmp) cc_final: 0.6626 (tpp) REVERT: C 519 MET cc_start: 0.9181 (ttm) cc_final: 0.8622 (tpt) REVERT: C 531 MET cc_start: 0.9077 (mmm) cc_final: 0.8748 (tpp) REVERT: C 578 MET cc_start: 0.8995 (pmm) cc_final: 0.8732 (tpt) REVERT: C 616 MET cc_start: 0.9695 (mtt) cc_final: 0.9314 (tpt) REVERT: C 659 PHE cc_start: 0.6297 (OUTLIER) cc_final: 0.6033 (m-80) REVERT: C 704 MET cc_start: 0.8087 (tmm) cc_final: 0.7243 (tmm) outliers start: 7 outliers final: 0 residues processed: 43 average time/residue: 0.0983 time to fit residues: 6.0057 Evaluate side-chains 30 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 77 optimal weight: 40.0000 chunk 280 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 308 optimal weight: 3.9990 chunk 306 optimal weight: 7.9990 chunk 173 optimal weight: 7.9990 chunk 344 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 282 optimal weight: 6.9990 chunk 198 optimal weight: 10.0000 chunk 259 optimal weight: 0.2980 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 GLN C 182 ASN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 829 GLN C 832 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.035305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.024237 restraints weight = 127734.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.024833 restraints weight = 88666.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.025284 restraints weight = 68063.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.025541 restraints weight = 56185.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.025777 restraints weight = 49698.991| |-----------------------------------------------------------------------------| r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 2.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 33912 Z= 0.184 Angle : 0.699 9.165 45680 Z= 0.402 Chirality : 0.044 0.399 4828 Planarity : 0.004 0.046 5840 Dihedral : 5.348 28.886 4392 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.04 % Favored : 93.76 % Rotamer: Outliers : 0.22 % Allowed : 3.40 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.13), residues: 3972 helix: -0.30 (0.10), residues: 2540 sheet: 1.20 (0.69), residues: 68 loop : -1.16 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 61 TYR 0.018 0.002 TYR D 721 PHE 0.022 0.002 PHE D 659 TRP 0.031 0.002 TRP A 757 HIS 0.005 0.001 HIS D 658 Details of bonding type rmsd covalent geometry : bond 0.00388 (33912) covalent geometry : angle 0.69858 (45680) hydrogen bonds : bond 0.05772 ( 1660) hydrogen bonds : angle 5.46618 ( 4773) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 MET cc_start: 0.9009 (mmp) cc_final: 0.8488 (mmm) REVERT: C 227 MET cc_start: 0.9486 (ptp) cc_final: 0.9137 (ptp) REVERT: C 290 MET cc_start: 0.9593 (tpt) cc_final: 0.9183 (tpp) REVERT: C 396 MET cc_start: 0.7705 (mmp) cc_final: 0.7325 (tpp) REVERT: C 531 MET cc_start: 0.9003 (mmm) cc_final: 0.8726 (mmt) REVERT: C 578 MET cc_start: 0.8979 (pmm) cc_final: 0.8728 (tpt) REVERT: C 616 MET cc_start: 0.9673 (mtt) cc_final: 0.9251 (tpp) REVERT: C 704 MET cc_start: 0.8073 (tmm) cc_final: 0.7430 (tmm) outliers start: 2 outliers final: 0 residues processed: 36 average time/residue: 0.0998 time to fit residues: 5.1720 Evaluate side-chains 29 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 268 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 12 optimal weight: 0.0000 chunk 286 optimal weight: 5.9990 chunk 321 optimal weight: 0.8980 chunk 343 optimal weight: 1.9990 chunk 298 optimal weight: 0.2980 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 287 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 GLN ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN ** C 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.037600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.027688 restraints weight = 134828.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.028322 restraints weight = 88523.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.028759 restraints weight = 64320.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.029132 restraints weight = 52009.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.029387 restraints weight = 44729.882| |-----------------------------------------------------------------------------| r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 2.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33912 Z= 0.133 Angle : 0.642 10.835 45680 Z= 0.368 Chirality : 0.042 0.278 4828 Planarity : 0.004 0.045 5840 Dihedral : 5.032 27.324 4392 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.14 % Favored : 94.66 % Rotamer: Outliers : 0.22 % Allowed : 2.96 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.13), residues: 3972 helix: -0.08 (0.10), residues: 2544 sheet: 0.49 (0.53), residues: 108 loop : -1.24 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 892 TYR 0.013 0.001 TYR B 482 PHE 0.028 0.002 PHE C 659 TRP 0.024 0.002 TRP A 757 HIS 0.003 0.001 HIS D 118 Details of bonding type rmsd covalent geometry : bond 0.00265 (33912) covalent geometry : angle 0.64169 (45680) hydrogen bonds : bond 0.05616 ( 1660) hydrogen bonds : angle 5.25889 ( 4773) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 124 MET cc_start: 0.8988 (mmp) cc_final: 0.8531 (mmm) REVERT: C 227 MET cc_start: 0.9453 (ptp) cc_final: 0.9027 (ptp) REVERT: C 290 MET cc_start: 0.9564 (tpt) cc_final: 0.9139 (tpp) REVERT: C 396 MET cc_start: 0.7443 (mmp) cc_final: 0.7146 (tpp) REVERT: C 545 LEU cc_start: 0.9522 (mt) cc_final: 0.9254 (mp) REVERT: C 578 MET cc_start: 0.9012 (pmm) cc_final: 0.8780 (tpt) REVERT: C 616 MET cc_start: 0.9680 (mtt) cc_final: 0.9230 (tpp) REVERT: C 704 MET cc_start: 0.7967 (tmm) cc_final: 0.7359 (tmm) outliers start: 2 outliers final: 0 residues processed: 39 average time/residue: 0.0903 time to fit residues: 5.1725 Evaluate side-chains 29 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 80 optimal weight: 7.9990 chunk 237 optimal weight: 4.9990 chunk 175 optimal weight: 6.9990 chunk 376 optimal weight: 0.1980 chunk 24 optimal weight: 0.0570 chunk 179 optimal weight: 0.0050 chunk 221 optimal weight: 0.0010 chunk 390 optimal weight: 1.9990 chunk 107 optimal weight: 0.0870 chunk 313 optimal weight: 2.9990 chunk 311 optimal weight: 0.0670 overall best weight: 0.0434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN C 477 ASN ** C 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.036133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.024954 restraints weight = 122492.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.025569 restraints weight = 84788.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.026006 restraints weight = 65432.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.026277 restraints weight = 54655.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.026509 restraints weight = 48347.982| |-----------------------------------------------------------------------------| r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 2.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 33912 Z= 0.134 Angle : 0.648 11.621 45680 Z= 0.366 Chirality : 0.042 0.271 4828 Planarity : 0.004 0.062 5840 Dihedral : 4.923 27.618 4392 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.24 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.13), residues: 3972 helix: 0.11 (0.10), residues: 2496 sheet: 0.65 (0.54), residues: 108 loop : -0.94 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 892 TYR 0.018 0.001 TYR A 193 PHE 0.028 0.001 PHE A 659 TRP 0.023 0.001 TRP A 757 HIS 0.003 0.000 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00263 (33912) covalent geometry : angle 0.64790 (45680) hydrogen bonds : bond 0.05403 ( 1660) hydrogen bonds : angle 5.13941 ( 4773) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 124 MET cc_start: 0.9050 (mmp) cc_final: 0.8510 (mmm) REVERT: C 227 MET cc_start: 0.9467 (ptp) cc_final: 0.9074 (ptp) REVERT: C 290 MET cc_start: 0.9620 (tpt) cc_final: 0.9180 (tpp) REVERT: C 545 LEU cc_start: 0.9503 (mt) cc_final: 0.9249 (mp) REVERT: C 578 MET cc_start: 0.9044 (pmm) cc_final: 0.8808 (tpt) REVERT: C 616 MET cc_start: 0.9695 (mtt) cc_final: 0.9366 (tpt) REVERT: C 702 ASN cc_start: 0.8654 (p0) cc_final: 0.8419 (t0) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0769 time to fit residues: 4.2337 Evaluate side-chains 29 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 365 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 392 optimal weight: 0.0670 chunk 24 optimal weight: 8.9990 chunk 251 optimal weight: 0.8980 chunk 232 optimal weight: 7.9990 chunk 344 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 overall best weight: 2.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN C 658 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.037281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.027280 restraints weight = 136845.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.027934 restraints weight = 90498.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.028411 restraints weight = 66958.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.028673 restraints weight = 54640.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.028901 restraints weight = 47913.331| |-----------------------------------------------------------------------------| r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 2.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 33912 Z= 0.151 Angle : 0.654 12.118 45680 Z= 0.373 Chirality : 0.041 0.169 4828 Planarity : 0.004 0.041 5840 Dihedral : 4.967 27.359 4392 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.04 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.13), residues: 3972 helix: -0.01 (0.10), residues: 2540 sheet: -0.14 (0.49), residues: 108 loop : -0.84 (0.18), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 760 TYR 0.027 0.001 TYR D 482 PHE 0.022 0.002 PHE B 659 TRP 0.024 0.002 TRP D 757 HIS 0.003 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00316 (33912) covalent geometry : angle 0.65416 (45680) hydrogen bonds : bond 0.05003 ( 1660) hydrogen bonds : angle 5.26422 ( 4773) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 124 MET cc_start: 0.8917 (mmp) cc_final: 0.8349 (mmm) REVERT: C 227 MET cc_start: 0.9411 (ptp) cc_final: 0.9039 (ptp) REVERT: C 290 MET cc_start: 0.9543 (tpt) cc_final: 0.9237 (tpp) REVERT: C 396 MET cc_start: 0.8214 (tpt) cc_final: 0.7777 (tpp) REVERT: C 578 MET cc_start: 0.9078 (pmm) cc_final: 0.8854 (tpt) REVERT: C 616 MET cc_start: 0.9695 (mtt) cc_final: 0.9270 (tpp) REVERT: C 704 MET cc_start: 0.7779 (tmm) cc_final: 0.6959 (tmm) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0803 time to fit residues: 3.9855 Evaluate side-chains 27 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 254 optimal weight: 7.9990 chunk 191 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 211 optimal weight: 0.0030 chunk 178 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 103 optimal weight: 0.0570 chunk 149 optimal weight: 0.3980 chunk 3 optimal weight: 0.3980 chunk 242 optimal weight: 2.9990 overall best weight: 0.3508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 GLN C 351 ASN C 477 ASN C 654 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.038020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.028118 restraints weight = 133100.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.028780 restraints weight = 87289.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.029274 restraints weight = 64338.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.029545 restraints weight = 52342.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.029816 restraints weight = 45760.877| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 2.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 33912 Z= 0.124 Angle : 0.636 12.862 45680 Z= 0.359 Chirality : 0.041 0.165 4828 Planarity : 0.004 0.050 5840 Dihedral : 4.806 26.724 4392 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.04 % Favored : 94.76 % Rotamer: Outliers : 0.11 % Allowed : 1.21 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.13), residues: 3972 helix: 0.10 (0.10), residues: 2536 sheet: 0.08 (0.50), residues: 108 loop : -0.84 (0.18), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 892 TYR 0.019 0.001 TYR D 482 PHE 0.039 0.001 PHE D 659 TRP 0.023 0.001 TRP B 757 HIS 0.003 0.000 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00244 (33912) covalent geometry : angle 0.63593 (45680) hydrogen bonds : bond 0.05029 ( 1660) hydrogen bonds : angle 5.08692 ( 4773) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 124 MET cc_start: 0.8897 (mmp) cc_final: 0.8377 (mmm) REVERT: C 227 MET cc_start: 0.9469 (ptp) cc_final: 0.9060 (ptp) REVERT: C 290 MET cc_start: 0.9589 (tpt) cc_final: 0.9267 (tpp) REVERT: C 396 MET cc_start: 0.8111 (tpt) cc_final: 0.7855 (tpp) REVERT: C 531 MET cc_start: 0.8940 (mmm) cc_final: 0.8552 (mtp) REVERT: C 569 MET cc_start: 0.8614 (mmm) cc_final: 0.8090 (mmm) REVERT: C 616 MET cc_start: 0.9697 (mtt) cc_final: 0.9246 (tpp) REVERT: C 704 MET cc_start: 0.7994 (tmm) cc_final: 0.7205 (tmm) REVERT: C 936 MET cc_start: 0.8220 (mtm) cc_final: 0.5313 (pmm) REVERT: C 1001 MET cc_start: 0.9100 (mmp) cc_final: 0.8896 (mmp) outliers start: 1 outliers final: 1 residues processed: 35 average time/residue: 0.0816 time to fit residues: 4.4868 Evaluate side-chains 28 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 170 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 294 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 274 optimal weight: 8.9990 chunk 353 optimal weight: 9.9990 chunk 204 optimal weight: 0.0030 chunk 23 optimal weight: 30.0000 chunk 149 optimal weight: 0.7980 chunk 331 optimal weight: 10.0000 chunk 38 optimal weight: 0.0030 overall best weight: 2.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.037596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.027719 restraints weight = 134932.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.028361 restraints weight = 89278.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.028839 restraints weight = 66878.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.029179 restraints weight = 54877.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.029363 restraints weight = 47657.590| |-----------------------------------------------------------------------------| r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 2.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 33912 Z= 0.134 Angle : 0.626 12.970 45680 Z= 0.359 Chirality : 0.040 0.156 4828 Planarity : 0.004 0.058 5840 Dihedral : 4.766 27.798 4392 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.34 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.13), residues: 3972 helix: 0.16 (0.10), residues: 2540 sheet: -0.02 (0.50), residues: 108 loop : -0.69 (0.18), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 892 TYR 0.022 0.001 TYR B 482 PHE 0.031 0.001 PHE A 659 TRP 0.023 0.001 TRP B 757 HIS 0.002 0.001 HIS D 118 Details of bonding type rmsd covalent geometry : bond 0.00279 (33912) covalent geometry : angle 0.62615 (45680) hydrogen bonds : bond 0.04711 ( 1660) hydrogen bonds : angle 5.07904 ( 4773) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: C 124 MET cc_start: 0.8797 (mmp) cc_final: 0.8276 (mmm) REVERT: C 227 MET cc_start: 0.9412 (ptp) cc_final: 0.8976 (ptp) REVERT: C 290 MET cc_start: 0.9516 (tpt) cc_final: 0.9228 (tpp) REVERT: C 396 MET cc_start: 0.8318 (tpt) cc_final: 0.7961 (tpp) REVERT: C 531 MET cc_start: 0.8978 (mmm) cc_final: 0.8621 (mtp) REVERT: C 616 MET cc_start: 0.9672 (mtt) cc_final: 0.9241 (tpp) REVERT: C 704 MET cc_start: 0.7732 (tmm) cc_final: 0.7016 (tmm) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0798 time to fit residues: 3.8002 Evaluate side-chains 28 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 86 optimal weight: 0.0370 chunk 227 optimal weight: 0.4980 chunk 45 optimal weight: 0.6980 chunk 302 optimal weight: 0.5980 chunk 146 optimal weight: 10.0000 chunk 181 optimal weight: 0.5980 chunk 338 optimal weight: 0.8980 chunk 207 optimal weight: 0.4980 chunk 154 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 104 optimal weight: 0.5980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 477 ASN C 939 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.038142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.028259 restraints weight = 132945.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.028908 restraints weight = 88216.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.029345 restraints weight = 65358.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.029733 restraints weight = 53411.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.029914 restraints weight = 46122.194| |-----------------------------------------------------------------------------| r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 2.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 33912 Z= 0.123 Angle : 0.636 13.399 45680 Z= 0.358 Chirality : 0.041 0.155 4828 Planarity : 0.004 0.056 5840 Dihedral : 4.703 26.810 4392 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.93 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.13), residues: 3972 helix: 0.19 (0.10), residues: 2540 sheet: 0.16 (0.50), residues: 108 loop : -0.69 (0.18), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 892 TYR 0.021 0.001 TYR B 482 PHE 0.032 0.001 PHE C 659 TRP 0.023 0.001 TRP A 757 HIS 0.003 0.000 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00245 (33912) covalent geometry : angle 0.63588 (45680) hydrogen bonds : bond 0.04776 ( 1660) hydrogen bonds : angle 4.99740 ( 4773) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 124 MET cc_start: 0.8894 (mmp) cc_final: 0.8350 (mmm) REVERT: C 290 MET cc_start: 0.9570 (tpt) cc_final: 0.9311 (tpp) REVERT: C 396 MET cc_start: 0.8315 (tpt) cc_final: 0.8101 (tpp) REVERT: C 519 MET cc_start: 0.8741 (tpt) cc_final: 0.8075 (ppp) REVERT: C 531 MET cc_start: 0.8944 (mmm) cc_final: 0.8631 (mtt) REVERT: C 569 MET cc_start: 0.8580 (mmm) cc_final: 0.8053 (mmm) REVERT: C 616 MET cc_start: 0.9710 (mtt) cc_final: 0.9260 (tpp) REVERT: C 913 MET cc_start: 0.9197 (ppp) cc_final: 0.8951 (ppp) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0715 time to fit residues: 3.5336 Evaluate side-chains 26 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 113 optimal weight: 7.9990 chunk 76 optimal weight: 20.0000 chunk 315 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 378 optimal weight: 0.3980 chunk 392 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 162 optimal weight: 0.5980 chunk 59 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.037946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.027990 restraints weight = 133429.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.028632 restraints weight = 89078.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.029052 restraints weight = 66884.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.029435 restraints weight = 54708.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.029610 restraints weight = 47298.563| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 2.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 33912 Z= 0.122 Angle : 0.625 13.581 45680 Z= 0.353 Chirality : 0.040 0.157 4828 Planarity : 0.004 0.058 5840 Dihedral : 4.646 27.036 4392 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.83 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.13), residues: 3972 helix: 0.26 (0.10), residues: 2540 sheet: 0.11 (0.50), residues: 108 loop : -0.61 (0.18), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 892 TYR 0.021 0.001 TYR B 482 PHE 0.029 0.001 PHE C 659 TRP 0.022 0.001 TRP A 757 HIS 0.002 0.000 HIS D 118 Details of bonding type rmsd covalent geometry : bond 0.00249 (33912) covalent geometry : angle 0.62524 (45680) hydrogen bonds : bond 0.04554 ( 1660) hydrogen bonds : angle 4.95928 ( 4773) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2423.88 seconds wall clock time: 44 minutes 14.22 seconds (2654.22 seconds total)